iCAGES main package

Please join the iCAGES mailing list at google groups here to receive announcements on software updates.

The latest version of iCAGES (2017Jan08) can be downloaded here.

iCAGES is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed.

Download

wget https://codeload.github.com/WangGenomicsLab/icages/tar.gz/(version)

Installation

  • Unzip downloaded file
tar -zxvf icages-(version).tar.gz
mv icages-(version) icages
  • Download and unzip database files
cd icages/
wget http://icages.wglab.org/download/icages/db.tar.gz
tar -zxvf db.tar.gz
  • Install necessary packages for perl. If you have root access, please use cpanm command to download JSON, HTTP::Request and LWP packages for perl
cpanm JSON
cpanm HTTP::Request
cpanm LWP
  • Install the first dependency for iCAGES, ANNOVAR. Please visit ANNOVAR website and download it. If your current direcotry is icages, then please move annovar/ directory to ./bin diretory
mv path-to-annovar/annovar/ ./bin/
  • Install the second dependency for iCAGES, DGIdb. If your current directory is icages, then please create a directory under ./bin directory and name it DGIdb.Please visit DGIdb to read about it and download download the corresponding perl script from here to ./bin/DGIdb directory
mkdir ./bin/DGIdb
wget https://raw.github.com/genome/dgi-db/master/files/perl_example.pl -O ./bin/DGIdb/getDrugList.pl
  • Please make some modifications of this get_DrugList.pl file. First, add this following line after "parse_opts();"
my $output;
open (OUT, ">$output") or die "iCAGES: cannot open file $output for writing the drugs recommended for cancer driver genes\n";
  • Then, add this following line after "'help' => \$help,"
'output:s'    => \$output 
  • Next, comment out this following line
print "gene_name\tdrug_name\tinteraction_type\tsource\tgene_categories\n";

into

# print "gene_name\tdrug_name\tinteraction_type\tsource\tgene_categories\n";
  • Next, change this following line
print "$gene_name\t$drug_name\t$interaction_type\t$source\t$gene_categories\n"; 

into

print OUT "$gene_name\t$drug_name\t$interaction_type\t$source\t$gene_categories\n"; 
  • And change this following lines
print "\n" . 'Unmatched search term: ', $_->{searchTerm}, "\n";
print 'Possible suggestions: ', join(",", @{$_->{suggestions}}), "\n";

into

print OUT "\n" . 'Unmatched search term: ', $_->{searchTerm}, "\n";
print OUT 'Possible suggestions: ', join(",", @{$_->{suggestions}}), "\n";
  • Install the third dependency for iCAGES, vcftools. Asuming you are already in icages-(version)/bin/ directory, download vcftools through sourceforge
wget http://iweb.dl.sourceforge.net/project/vcftools/vcftools_0.1.12b.tar.gz
tar -zxvf vcftools_0.1.12b.tar.gz 
mv vcftools_0.1.12b/ vcftools/
rm vcftools_0.1.12b.tar.gz
  • Install vcftools by typing the following command
cd vcftools
make
  • Install the fourth dependency for iCAGES, bedtools. Asuming you are already in icages-(version)/bin/ directory,
wget https://codeload.github.com/arq5x/bedtools2/tar.gz/v2.25.0
tar -zxvf v2.25.0.tar.gz
mv bedtools2-2.25.0 bedtools
rm v2.25.0.tar.gz
cd bedtools
make

Additional databases

Initial databases for iCAGES only includes hg19 reference genome for human. In order to annotate variants with hg18 or hg38 reference genomes, please download these additional databases compiled for these two versions of references.

  • hg18
cd icages/db/
wget http://icages.wglab.org/download/icages/hg18_db.tar.gz
tar -zxvf db_hg18.tar.gz
  • hg38
cd icages/db/
wget http://icages.wglab.org/download/icages/hg38_db.tar.gz
tar -zxvf db_hg18.tar.gz